Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships

Pairwise sequence comparison methods have been assessed using proteins whose relationships are known reliably from their structures and functions, as described in the scop database [Murzin, A. G., Brenner, S. E., Hubbard, T. & Chothia C. (1995) J. Mol. Biol. 247, 536–540]. The evaluation tested the programs blast [Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. (1990). J. Mol. Biol. 215, 403–410], wu-blast2 [Altschul, S. F. & Gish, W. (1996) Methods Enzymol. 266, 460–480], fasta [Pearson, W. R. & Lipman, D. J. (1988) Proc. Natl. Acad. Sci. USA 85, 2444–2448], and ssearch [Smith, T. F. & Waterman, M. S. (1981) J. Mol. Biol. 147, 195–197] and their scoring schemes. The error rate of all algorithms is greatly reduced by using statistical scores to evaluate matches rather than percentage identity or raw scores. The E-value statistical scores of ssearch and fasta are reliable: the number of false positives found in our tests agrees well with the scores reported. However, the P-values reported by blast and wu-blast2 exaggerate significance by orders of magnitude. ssearch, fasta ktup = 1, and wu-blast2 perform best, and they are capable of detecting almost all relationships between proteins whose sequence identities are >30%. For more distantly related proteins, they do much less well; only one-half of the relationships between proteins with 20–30% identity are found. Because many homologs have low sequence similarity, most distant relationships cannot be detected by any pairwise comparison method; however, those which are identified may be used with confidence.

Método da propagação de feixe de ângulo largo para análise de guias de ondas ópticos não-lineares

Este trabalho propõe uma extensão do método de propagação de feixe (BPM - Beam Propagation Method) para a análise de guias de ondas ópticos e acopladores baseados em materiais não-lineares do tipo Kerr. Este método se destina à investigação de estruturas onde a utilização da equação escalar de Helmholtz (EEH) em seu limite paraxial não mais se aplica. Os métodos desenvolvidos para este fim são denominados na literatura como métodos de propagação de feixe de ângulo largo. O formalismo aqui desenvolvido é baseado na técnica das diferenças finitas e nos esquemas de Crank-Nicholson (CN) e Douglas generalizado (GD). Estes esquemas apresentam como característica o fato de apresentarem um erro de truncamento em relação ao passo de discretização transversal, Δx, proporcional a O(Δx2) para o primeiro e O(Δx4). A convergência do método em ambos esquemas é otimizada pela utilização de um algoritmo interativo para a correção do campo no meio não-linear. O formalismo de ângulo largo é obtido pela expansão da EEH para os esquemas CN e GD em termos de polinômios aproximantes de Padé de ordem (1,0) e (1,1) para CN e GD, e (2,2) e (3,3) para CN. Os aproximantes de ordem superior a (1,1) apresentam sérios problemas de estabilidade. Este problema é eliminado pela rotação dos aproximantes no plano complexo. Duas condições de contorno nos extremos da janela computacional são também investigadas: 1) (TBC - Transparent Boundary Condition) e 2) condição de contorno absorvente (TAB - Transparent Absorbing Boundary). Estas condições de contorno possuem a facilidade de evitar que reflexões indesejáveis sejam transmitidas para dentro da janela computacional. Um estudo comparativo da influência destas condições de contorno na solução de guias de ondas ópticos não-lineares é também abordada neste trabalho.

Estudo de alterações estruturais cerebrais em pacientes com esquizofrenia crônica e de primeiro episódio através de imagens por ressonância magnética com morfometria baseada no voxel

Introdução: Embora alterações estruturais cerebrais na esquizofrenia venham sendo repetidamente demonstradas em estudos de ressonância magnética (RM), ainda permanece incerto se tais alterações são estáticas ou progressivas. Enquanto estudos longitudinais são tradicionalmente utilizados na avaliação da questão da progressão, estudos transversais de neuroimagem comparando diretamente pacientes com esquizofrenia crônica e de primeiro episódio a controles saudáveis têm sido bastante raros até o presente. Com o recente interesse em meganálises combinando dados multicêntricos de RM visando-se a maior poder estatístico, o presente estudo multicêntrico de morfometria baseada no voxel (VBM) foi realizado para avaliar os padrões de alterações estruturais cerebrais segundo os diferentes estágios da doença, bem como para avaliar quais (se alguma) dessas alterações se correlacionariam especificamente a moderadores clínicos potenciais, tais como exposição cumulativa a antipsicóticos, tempo de doença e gravidade da doença. Métodos: Selecionou-se uma ampla amostra de pacientes com esquizofrenia (161, sendo 99 crônicos e 62 de primeiro episódio) e controles (151) a partir de quatro estudos prévios de RM (1,5T) realizados na mesma região do Brasil. O processamento e análise das imagens foi realizado usando-se o software Statistical Parametric Mapping (SPM8) com emprego do algoritmo DARTEL (diffeomorphic anatomical registration through exponentiated Lie algebra). Os efeitos de grupo sobre os volumes regionais de substância cinzenta (SC) foram analisados através de comparações voxel-a-voxel por análises de covariância em modelos lineares gerais, inserindo-se, em todas as análises, o volume total de SC, protocolo do scanner, idade e sexo como variáveis de confusão. Por fim, foram realizadas análises de correlação entre os aludidos moderadores clínicos potenciais e os volumes cerebrais globais e regionais. Resultados: Os pacientes com esquizofrenia de primeiro episódio apresentaram reduções volumétricas sutis em comparação aos controles, em um circuito neural circunscrito e identificável apenas em análises SVC (small volume correction) [p < 0.05, com correção family-wise error (FWE)], incluindo a ínsula, estruturas têmporo-límbicas e corpo estriado. Os pacientes crônicos, por outro lado, apresentaram um padrão de alterações extensas comparativamente aos controles, envolvendo os córtices frontais orbitais, superiores e inferiores bilateralmente, córtex frontal médio direito, ambos os córtices cingulados anteriores, ambas as ínsulas, e os córtices temporais superior e médio direitos (p < 0.05, análises whole-brain com correção FWE). Foram encontradas correlações negativas significantes entre exposição cumulativa a antipsicóticos e volumes globais de SC e substância branca nos pacientes com esquizofrenia, embora as correlações com reduções regionais não tenham sido significantes. Detectaram-se, ainda, correlações negativas significantes entre tempo de doença e volumes regionais relativos da ínsula esquerda, córtex cingulado anterior direito e córtices pré-frontais dorsolaterais nas análises SVC para os grupos conjuntos (esquizofrenia crônica e de primeiro episódio). Conclusão: Os achados supracitados indicam que: a) as alterações estruturais associadas com o diagnóstico de esquizofrenia são mais disseminadas na forma crônica em comparação à de primeiro episódio; b) reduções volumétricas regionais em áreas específicas do cérebro podem variar em função do tempo de doença; c) a exposição cumulativa a antipsicóticos associou-se a alterações volumétricas globais, e não regionais

The Gaia-ESO Survey: processing FLAMES-UVES spectra

The Gaia-ESO Survey is a large public spectroscopic survey that aims to derive radial velocities and fundamental parameters of about 105 Milky Way stars in the field and in clusters. Observations are carried out with the multi-object optical spectrograph FLAMES, using simultaneously the medium-resolution (R ~ 20 000) GIRAFFE spectrograph and the high-resolution (R ~ 47 000) UVES spectrograph. In this paper we describe the methods and the software used for the data reduction, the derivation of the radial velocities, and the quality control of the FLAMES-UVES spectra. Data reduction has been performed using a workflow specifically developed for this project. This workflow runs the ESO public pipeline optimizing the data reduction for the Gaia-ESO Survey, automatically performs sky subtraction, barycentric correction and normalisation, and calculates radial velocities and a first guess of the rotational velocities. The quality control is performed using the output parameters from the ESO pipeline, by a visual inspection of the spectra and by the analysis of the signal-to-noise ratio of the spectra. Using the observations of the first 18 months, specifically targets observed multiple times at different epochs, stars observed with both GIRAFFE and UVES, and observations of radial velocity standards, we estimated the precision and the accuracy of the radial velocities. The statistical error on the radial velocities is σ ~ 0.4 km s-1 and is mainly due to uncertainties in the zero point of the wavelength calibration. However, we found a systematic bias with respect to the GIRAFFE spectra (~0.9 km s-1) and to the radial velocities of the standard stars (~0.5 km s-1) retrieved from the literature. This bias will be corrected in the future data releases, when a common zero point for all the set-ups and instruments used for the survey is be established.

Visual and optical performance and quality of life after implantation of posterior chamber phakic intraocular lens

Purpose To evaluate visual, optical, and quality of life (QoL) outcomes and intercorrelations after bilateral implantation of posterior chamber phakic intraocular lenses. Methods Twenty eyes with high to moderate myopia of 10 patients that underwent PRL implantation (Phakic Refractive Lens, Carl Zeiss Meditec AG) were examined. Refraction, visual acuity, photopic and low mesopic contrast sensitivity (CS) with and without glare, ocular aberrations, as well as QoL outcomes (National Eye Institute Refractive Error Quality of Life Instrument-42, NEI RQL-42) were evaluated at 12 months postoperatively. Results Significant improvement in uncorrected (UDVA) and best-corrected distance (CDVA) visual acuities were found postoperatively (p < 0.01), with significant reduction in spherical equivalent (p < 0.01). Low mesopic CS without glare was significantly better than measurements with glare for 1.5, 3, and 6 cycles/degree (p < 0.01). No significant correlations between higher order root mean square (RMS) with CDVA (r = −0.26, p = 0.27) and CS (r ≤ 0.45, p ≥ 0.05) were found. Postoperative binocular photopic CS for 12 cycles/degree and 18 cycles/degree correlated significantly with several RQL-42 scales. Glare index correlated significantly with CS measures and scotopic pupil size (r = −0.551, p = 0.04), but not with higher order RMS (r = −0.02, p = 0.94). Postoperative higher order RMS, postoperative primary coma and postoperative spherical aberration was significant higher for 5-mm pupil diameter (p < 0.01) compared with controls. Conclusions Correction of moderate to high myopia by means of PRL implantation had a positive impact on CS and QoL. The aberrometric increase induced by the surgery does not seem to limit CS and QoL. However, perception of glare is still a relevant disturbance in some cases possibly related to the limitation of the optical zone of the PRL.

Minimizing the IOL Power Error Induced by Keratometric Power

Purpose. To evaluate theoretically in normal eyes the influence on IOL power (PIOL) calculation of the use of a keratometric index (nk) and to analyze and validate preliminarily the use of an adjusted keratometric index (nkadj) in the IOL power calculation (PIOLadj). Methods. A model of variable keratometric index (nkadj) for corneal power calculation (Pc) was used for IOL power calculation (named PIOLadj). Theoretical differences ($PIOL) between the new proposed formula (PIOLadj) and which is obtained through Gaussian optics (PIOL Gauss) were determined using Gullstrand and Le Grand eye models. The proposed new formula for IOL power calculation (PIOLadj) was prevalidated clinically in 81 eyes of 81 candidates for corneal refractive surgery and compared with Haigis, HofferQ, Holladay, and SRK/T formulas. Results. A theoretical PIOL underestimation greater than 0.5 diopters was present in most of the cases when nk = 1.3375 was used. If nkadj was used for Pc calculation, a maximal calculated error in $PIOL of T0.5 diopters at corneal vertex in most cases was observed independently from the eye model, r1c, and the desired postoperative refraction. The use of nkadj in IOL power calculation (PIOLadj) could be valid with effective lens position optimization nondependent of the corneal power. Conclusions. The use of a single value of nk for Pc calculation can lead to significant errors in PIOL calculation that may explain some IOL power overestimations with conventional formulas. These inaccuracies can be minimized by using the new PIOLadj based on the algorithm of nkadj.

Relationship among Corneal Biomechanics, Refractive Error, and Axial Length

Purpose: To evaluate the relationship between different ocular and corneal biomechanical parameters in emmetropic and ametropic healthy white children. Methods: This study included 293 eyes of 293 healthy Spanish children (135 boys and 158 girls), ranging in age from 6 to 17 years. Subjects were divided according to the refractive error: control (emmetropia, 99 children), myopia (100 children), and hyperopia (94 children) groups. In all cases, corneal hysteresis (CH) and corneal resistance factor (CRF) were evaluated with the Ocular Response Analyzer system. Axial length (AL) and mean corneal power were also measured by partial coherence interferometry (IOLMaster), and central corneal thickness (CCT) and anterior chamber depth were measured by anterior segment optical coherence tomography (Visante). Results: Mean (±SD) CH and CRF were 12.12 (±1.71) and 12.30 (±1.89) mm Hg, respectively. Mean (±SD) CCT was 542.68 (±37.20) μm and mean (±SD) spherical equivalent was +0.14 (±3.41) diopters. A positive correlation was found between CH and CRF (p < 0.001), and both correlated as well with CCT (p < 0.0001). Corneal resistance factor was found to decrease with increasing age (p = 0.01). Lower levels of CH were associated with longer AL and more myopia (p < 0.001 and p = 0.001, respectively). Higher values of CH were associated with increasing hyperopia. Significant differences in CH were found between emmetropic and myopic groups (p < 0.001) and between myopic and hyperopic groups (p = 0.011). There were also significant differences in CRF between emmetropic and myopic groups (p = 0.02). Multiple linear regression analysis showed that lower CH and CRF significantly associated with thinner CCT, longer AL, and flatter corneal curvature. Conclusions: The Ocular Response Analyzer corneal biomechanical properties seem to be compromised in myopia from an early age, especially in high myopia.

Estimation of the Central Corneal Power in Keratoconus: Theoretical and Clinical Assessment of the Error of the Keratometric Approach

Purpose: The aim of this study was to analyze theoretically the errors in the central corneal power calculation in eyes with keratoconus when a keratometric index (nk) is used and to clinically confirm the errors induced by this approach. Methods: Differences (DPc) between central corneal power estimation with the classical nk (Pk) and with the Gaussian equation (PGauss c ) in eyes with keratoconus were simulated and evaluated theoretically, considering the potential range of variation of the central radius of curvature of the anterior (r1c) and posterior (r2c) corneal surfaces. Further, these differences were also studied in a clinical sample including 44 keratoconic eyes (27 patients, age range: 14–73 years). The clinical agreement between Pk and PGauss c (true net power) obtained with a Scheimpflug photography–based topographer was evaluated in such eyes. Results: For nk = 1.3375, an overestimation was observed in most cases in the theoretical simulations, with DPc ranging from an underestimation of 20.1 diopters (D) (r1c = 7.9 mm and r2c = 8.2 mm) to an overestimation of 4.3 D (r1c = 4.7 mm and r2c = 3.1 mm). Clinically, Pk always overestimated the PGauss c given by the topography system in a range between 0.5 and 2.5 D (P , 0.01). The mean clinical DPc was 1.48 D, with limits of agreement of 0.71 and 2.25 D. A very strong statistically significant correlation was found between DPc and r2c (r = 20.93, P , 0.01). Conclusions: The use of a single value for nk for the calculation of corneal power is imprecise in keratoconus and can lead to significant clinical errors.

Error induced by the estimation of the corneal power and the effective lens position with a rotationally asymmetric refractive multifocal intraocular lens

AIM: To evaluate the prediction error in intraocular lens (IOL) power calculation for a rotationally asymmetric refractive multifocal IOL and the impact on this error of the optimization of the keratometric estimation of the corneal power and the prediction of the effective lens position (ELP). METHODS: Retrospective study including a total of 25 eyes of 13 patients (age, 50 to 83y) with previous cataract surgery with implantation of the Lentis Mplus LS-312 IOL (Oculentis GmbH, Germany). In all cases, an adjusted IOL power (PIOLadj) was calculated based on Gaussian optics using a variable keratometric index value (nkadj) for the estimation of the corneal power (Pkadj) and on a new value for ELP (ELPadj) obtained by multiple regression analysis. This PIOLadj was compared with the IOL power implanted (PIOLReal) and the value proposed by three conventional formulas (Haigis, Hoffer Q and Holladay). RESULTS: PIOLReal was not significantly different than PIOLadj and Holladay IOL power (P>0.05). In the Bland and Altman analysis, PIOLadj showed lower mean difference (-0.07 D) and limits of agreement (of 1.47 and -1.61 D) when compared to PIOLReal than the IOL power value obtained with the Holladay formula. Furthermore, ELPadj was significantly lower than ELP calculated with other conventional formulas (P<0.01) and was found to be dependent on axial length, anterior chamber depth and Pkadj. CONCLUSION: Refractive outcomes after cataract surgery with implantation of the multifocal IOL Lentis Mplus LS-312 can be optimized by minimizing the keratometric error and by estimating ELP using a mathematical expression dependent on anatomical factors.

Comparison of the predictability of refractive cylinder correction by laser in situ keratomileusis in eyes with low or high ocular residual astigmatism

Purpose: To compare the manifest refractive cylinder (MRC) predictability of myopic astigmatism laser in situ keratomileusis (LASIK) between eyes with low and high ocular residual astigmatism (ORA). Setting: London Vision Clinic, London, United Kingdom. Design: Retrospective case study. Methods: The ORA was considered the vector difference between the MRC and the corneal astigmatism. The index of success (IoS), difference vector ÷ MRC, was analyzed for different groups as follows: stage 1, low ORA (ORA ÷ MRC <1), high ORA (ORA ÷ MRC ≥1); stage 2, low ORA group reduced to match the high ORA group for MRC; stage 3, grouped by ORA magnitude with low ORA (<0.50 diopters [D]), mid ORA (0.50 to 1.24 D), and high ORA (≥1.25 D); stage 4, high ORA group subdivided into low (<0.75 D) and high (≥0.75 D) corneal astigmatism. Results: For stage 1, the mean preoperative MRC and mean IoS were −1.32 D ± 0.65 (SD) (range −0.55 to −3.77 D) and 0.27, respectively, for low ORA and −0.79 ± 0.20 D (range −0.56 to −2.05 D) and 0.37, respectively, for high ORA. For stage 2, the mean IoS increased to 0.32 for low ORA. For stage 3, the mean IoS was 0.28, 0.29, and 0.31 for low ORA, mid ORA, and high ORA, respectively. For stage 4, the mean IoS was 0.20 for high ORA/low corneal astigmatism and 0.35 for high ORA/high corneal astigmatism. Conclusions: The MRC predictability was slightly worse in eyes with high ORA when grouped by the ORA ÷ MRC. Matching for the MRC and grouping by ORA magnitude resulted in similar predictability; however, eyes with high ORA and high corneal astigmatism were less predictable.

3DCOMET: 3D compression methods test dataset

The use of 3D data in mobile robotics applications provides valuable information about the robot’s environment. However usually the huge amount of 3D information is difficult to manage due to the fact that the robot storage system and computing capabilities are insufficient. Therefore, a data compression method is necessary to store and process this information while preserving as much information as possible. A few methods have been proposed to compress 3D information. Nevertheless, there does not exist a consistent public benchmark for comparing the results (compression level, distance reconstructed error, etc.) obtained with different methods. In this paper, we propose a dataset composed of a set of 3D point clouds with different structure and texture variability to evaluate the results obtained from 3D data compression methods. We also provide useful tools for comparing compression methods, using as a baseline the results obtained by existing relevant compression methods.

Multinomial goodness-of-fit: large sample tests with survey design correction and exact tests for small samples

A new Stata command called -mgof- is introduced. The command is used to compute distributional tests for discrete (categorical, multinomial) variables. Apart from classic large sample $\chi^2$-approximation tests based on Pearson's $X^2$, the likelihood ratio, or any other statistic from the power-divergence family (Cressie and Read 1984), large sample tests for complex survey designs and exact tests for small samples are supported. The complex survey correction is based on the approach by Rao and Scott (1981) and parallels the survey design correction used for independence tests in -svy:tabulate-. The exact tests are computed using Monte Carlo methods or exhaustive enumeration. An exact Kolmogorov-Smirnov test for discrete data is also provided.

FISICO: Fast Image SegmentatIon COrrection.

BACKGROUND AND PURPOSE In clinical diagnosis, medical image segmentation plays a key role in the analysis of pathological regions. Despite advances in automatic and semi-automatic segmentation techniques, time-effective correction tools are commonly needed to improve segmentation results. Therefore, these tools must provide faster corrections with a lower number of interactions, and a user-independent solution to reduce the time frame between image acquisition and diagnosis. METHODS We present a new interactive method for correcting image segmentations. Our method provides 3D shape corrections through 2D interactions. This approach enables an intuitive and natural corrections of 3D segmentation results. The developed method has been implemented into a software tool and has been evaluated for the task of lumbar muscle and knee joint segmentations from MR images. RESULTS Experimental results show that full segmentation corrections could be performed within an average correction time of 5.5±3.3 minutes and an average of 56.5±33.1 user interactions, while maintaining the quality of the final segmentation result within an average Dice coefficient of 0.92±0.02 for both anatomies. In addition, for users with different levels of expertise, our method yields a correction time and number of interaction decrease from 38±19.2 minutes to 6.4±4.3 minutes, and 339±157.1 to 67.7±39.6 interactions, respectively.

Error estimation and iterative improvement for the numerical solution of operator equations /

Bibliography: p. 85-87.

An analysis of burst encoding methods and transmission properties /

Thesis (M. S.)--University of Illinois at Urbana-Champaign.